


Atlantis' Choice

by respoftw



Category: Stargate Atlantis
Genre: Ambiguous/Open Ending, Angst, M/M, Sentient Atlantis
Language: English
Status: Completed
Published: 2019-02-09
Updated: 2019-02-09
Packaged: 2019-10-25 04:09:46
Rating: Not Rated
Warnings: No Archive Warnings Apply
Chapters: 1
Words: 1,664
Publisher: archiveofourown.org
Story URL: https://archiveofourown.org/works/17717774
Author URL: https://archiveofourown.org/users/respoftw/pseuds/respoftw
Summary: “The AI that is Atlantis has been present since we first came through the gate but it, I mean they were  - - there’s not enough power to really let Atlantis behave as they’re supposed to.  I mean, we could keep the lights on, keep them floating, keep them running but we’ve always known that Atlantis could do more.  Could be more.”“And now we have the ZPMs?” Lorne asked.“All bets are off.”





	Atlantis' Choice

McKay and Zelenka had apparently submitted a report about the avatar sub-routine back in their first year on Atlantis; the product of a chance find in the database that nobody ever truly thought they would see become relevant.

Had Elizabeth still been in charge, they might not have even remembered it.  If Sam were still in charge, they definitely wouldn't have. Woolsey was different though. Woolsey had lasted longer in charge than Sam and Elizabeth in combined and his attention to detail, his love of the minutiae, meant that the report was remembered.

It meant they had time to prepare.

“So, what happens?  When Atlantis is fully powered.  Explain it to me.” John looked around the table, his hands laid out in front of him.  It was all he could do not to curl his knuckles into a fist and punch something. Finding six fully charged ZPMs when the Wraith were on their way was supposed to be a good thing, they had all thought it was the best thing ever until Woolsey had held up a giant red stop sign in the form of a seven-year-old report that McKay and Zelenka barely remembered.

“I’m sure it will come as no surprise to any of you that Atlantis is sentient.”

Everyone around the table, John included, nodded at Radek’s words. Atlantis may not speak but anyone with the gene who had spent more than a couple of hours on the city knew - deep down in their bones knew - that the city was alive. 

“The AI that is Atlantis' programming has been present since we first came through the gate but it, I mean  _ they _ were  - - there’s not enough power to really let Atlantis behave as  _ they’re _ supposed to.  I mean, we could keep the lights on, keep them floating, keep them running but we’ve always known that Atlantis could do more.  Could _be_ more.”

“And now that we have the ZPMs?” Lorne asked.

Radek grimaced.  “All bets are off.”

“The entries you found on the database indicated that the city used to function with the help of an avatar,” Woolsey said.  “If the city truly is sentient, and I find that in my time here I have come to believe that as fact, then why isn’t the avatar some kind of - of -” Woolsey seemed to struggle to find the right words for what  _ should _ have been.

“Some kind of a hologram like the doctor on _Voyager_?” Lorne suggested.  

“Precisely.”

Zelenka pushed his glasses up before answering.  “We believe that the Ancients wanted to temper the power they gave the AI.  A human avatar, while linked to the city, would be able to exert some measure of control over Atlantis.  It is not an overtaking, more like a -”

“A mind meld,” John finished, continuing with the Star Trek theme.

“A permanent one, aye.”  Carson cleared his throat.  “I’ve examined the entries that Rodney and Radek found and the meld if that’s what we’re calling it is, well, it’s beyond our ken really.  What I _can_ say is that there would be no reversing it once it’s done. The changes to the brain chemistry - - the neural pathways of the avatar are completely rewritten.”

“Are you saying that the - the person that the city chooses will no longer be human?” Teyla asked quietly.  

John shifted in his chair, feeling strangely uncomfortable about the way everyone was very studiously _not_ looking at him.  Well, everyone but Rodney that was. Rodney’s eyes were red with too many hours awake and they never moved from John; hadn’t since Woolsey had called this damn meeting.

“They wouldn’t _ not  _ be human but they would be...more.  Something different.”

“Would they still be themselves?”  Ronon asked the question that John really wanted to know the answer to and John felt his lungs constrict as he waited for the answer.

“We think so,” Radek answered, letting John breath again.  “The database included journal entries of a former avatar, from both before and after his joining and they seem to be similar enough in tone to indicate a retained sense of self.”

John smiled weakly.  “Well, that’s good, right?”

“It is,” Radek agreed.  “But there  _ were _ side effects.  Significant ones.”

“I believe we would all like to hear them,” Teyla said.  “Please.”

“Whoever the city chooses would be - they would become part of the city in much the same way the AI is part of the city.  If we were ever to lose power enough that the connection to the avatar failed - - or if the city was destroyed then..”

Radek didn’t need to finish.  They could all follow that through to its logical conclusion.  

“Well, we’ve managed this long without blowing Atlantis up,” John interrupted the gloomy silence. “What else?”

It was Carson who continued.  “Records indicate that the chosen avatar lost their eyesight."

There was a sharp intake of breath at that but John’s eyes were closed so he didn’t know who it came from.  Carson ignored it and continued. 

“At least, in a manner of speaking.  Atlantis would feed optical information directly into the avatar’s brain so they could still function.  Some might argue that they would be able to see better than they ever could. The same with hearing. Atlantis would provide the data for any auditory processing as well.  They would still age, albeit at a slower age. While they could still eat and sleep they wouldn’t necessarily need to as Atlantis would provide the energy for them to function.”

“Could they leave the city?  I mean, the way you’re talking it sounds like - - could they go through that gate?”  John heard the desperation in his voice and he knew he should be embarrassed but no-one was looking at him and he really needed the answer to be yes.

There was a moment of silence before Rodney spoke, his voice sounding wrecked.  “We think you would still be able to fly the jumpers. Even when they’re off world they are still connected to the city, or at least they will be when we have full power.  I don’t know that you would be able to leave the jumper but you would still be able to fly.”

John drew in a shaky breath.  It was the first time anyone had dropped the ‘whoever Atlantis chooses’ schtick and he knew it had been coming, knew they had all been thinking it but it still felt like a punch to the gut.  The knowledge that he would still be able to fly took the edge off though, just like Rodney must have known it would.

“When are the Wraith ships gonna be here?” he asked, even though he knew the answer.

“Two days, Sir.”

“And how long before we need to have the ZPMs in place?”

“If we want to survive?” Rodney asked.  “We should have already installed them. We already would have if this hadn’t..”

John nodded.  He stood, his chair scraping against the ceramic tile of Atlantis.  He wondered if he’d be able to feel that when he was connected to the city.  Did that count as damage? Would it hurt?

“I take it you want me in the chair when this happens?”

Carson nodded.  “Aye, lad. I think that would be best.”

“Ok, let’s do this.”

* * *

There wasn’t time for any kind of goodbye.  A quick forehead touch with Teyla, a backslap from Ronon, a nod from Lorne and John found himself settling into the control chair while Carson hooked him up to a monitor and Rodney and Radek prepared the ZPMs.

“Are you sure about this?”

John did his best to smile for Carson.  “Hey, I’ll still be me, remember?”

“Yes, but - “

“Atlantis is my home,” John said, breathing the fear away. “She wouldn’t hurt me.”

“We are ready, Colonel,”  Radek said. “ZPM activation in 10 - 9 - “

“Wait, wait, wait, wait,” Rodney left his post at the ZPM station and stumbled across to the chair.  John sat up, pulling at the wires Carson had attached to him and pulled Rodney close. 

“I know, buddy,” he breathed, nosing into Rodney’s neck.  “I’ll still be me.”

“Stupid,” Rodney muttered.  “So fucking stupid. I should have told you that - - you’re the best thing in my life. I’ve loved you for a stupidly, stupidly long time and - - “

Rodney’s mouth on his was desperate and John wished it didn’t feel so much like a goodbye.  

“I love you too,” he whispered back in between hard, bruising kisses.  “This won’t change that, I’ll still be me.”

“Rodney, John, I am sorry but - - “

John felt Ronon’s hands pulling them apart and he knew that they needed to stop but it wasn’t fair.  It was too soon - it wasn’t fair - it was - - 

“I’ll still be me.  I’ll still be me. I’ll still be me.”

John repeated it like a mantra as the ZPM initiation began.  He kept his eyes on Rodney the entire time until Radek’s countdown approached zero.  Then, he squeezed his eyes shut and hoped harder than he ever had in his life that everything would work out alright and - - “

“RODNEY!!”

John’s eyes sprang open at Radek’s yell, in time enough to see Rodney spasm as if hit by lightning.  John was out of the chair in an instant but found himself repelled by the forcefield that had sprung around Rodney.  Rodney’s mouth was open in a silent scream and John knew what was happening immediately, felt stupid that they all hadn’t realised that this was the way it was always going to go.

John might have the gene.  He might be genetically predisposed to be the most compatible with Atlantis but it was Rodney who loved the city; Rodney who fixed the city, Rodney who knew Atlantis better than anyone else in two galaxies.

It seemed obvious now that it was slapping them in the face.  Every bit of data they could find said it was the city’s choice.  

Of course, the city would choose Rodney.

_Oh, God,_ John thought. _Let him still be Rodney._

**Author's Note:**

> No, I am not dead! It seems a long time since I've posted. Sorry about that. So here, have a way angstier than I intended fic about Atlantis preferring Rodney over John.
> 
> Sigh, I really must get back to writing fluff!!


End file.
